Preheat the oven to 350 degrees F (175 degrees C). Spray a 9x13-inch casserole dish with cooking spray.
Mix refried beans, 1 1/2 cups cheese, and onion in a microwave-safe bowl. Microwave on high until cheese is melted, about 1 minute.
Stack three tortillas on a microwave-safe plate; microwave on high until warm, about 30 seconds. Repeat to warm remaining tortillas.
Pour enough enchilada sauce onto a small plate to cover. Quickly dip both sides of one tortilla in sauce. Spoon bean filling down the middle, then wrap tortilla around filling. Place into the prepared baking dish. Repeat to dip, fill, and roll remining tortillas.
Pour remaining enchilada sauce over filled tortillas and sprinkle with remaining cheese. Cover the dish with aluminum foil.
Bake in the preheated oven until sauce is bubbling and cheese is melted, 35 and 40 minutes.